Comments (4)
sidneymbell
commented on May 30, 2024
1
Ach! Thank you. I've been running SC2 builds for so long where we have the
`keep_polytomies` flag on by default that I forgot I need to add it
explicitly. Let me iterate a bit here.
…On Tue, Oct 11, 2022 at 3:46 AM Cornelius Roemer ***@***.***> wrote:
Hi @sidneymbell <https://github.com/sidneymbell>, great to see you're
making good progress!
I think this is a bit of an A-B problem. While Nextclade should be able to
work with these nested trees, it's best to not resolve polytomies in the
creation of the tree anyways. This makes it lighter on Nextclade and the
polytomy resolution without mutations on branches is not that helpful for
anything Nextclade does anyways.
Do you know what I mean? It's a setting in augur refine. None of the
current dataset trees resolve polytomies. This is a great thing to add to a
future dataset contributor guide :)
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ivan-aksamentov
commented on May 30, 2024
@sidneymbell Oh no! How strange.
Yes, please drop me on Trevor's Slack all the files required to run the command to reproduce the error. I'll investigate.
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sidneymbell
commented on May 30, 2024
Sent! Thanks @ivan-aksamentov
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corneliusroemer
commented on May 30, 2024
Hi @sidneymbell, great to see you're making good progress!
I think this is a bit of an A-B problem. While Nextclade should be able to work with these nested trees, it's best to not resolve polytomies in the creation of the tree anyways. This makes it lighter on Nextclade and the polytomy resolution without mutations on branches is not that helpful for anything Nextclade does anyways.
Do you know what I mean? It's a setting in augur refine. None of the current dataset trees resolve polytomies. This is a great thing to add to a future dataset contributor guide :)
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